MycoCosm portal: gearing up for 1000 fungal genomes
Open accessAbstract
MycoCosm is a fungal genomics portal (http://jgi.doe.gov/fungi), developed by the US Department of Energy Joint Genome Institute to support integration, analysis and dissemination of fungal genome sequences and other 'omics' data by providing interactive web-based tools. MycoCosm also promotes and facilitates user community participation through the nomination of new species of fungi for sequencing, and the annotation and analysis of resulting data. By efficiently filling gaps in the Fungal Tree of Life, MycoCosm will help address important problems associated with energy and the environment, taking advantage of growing fungal genomics resources.
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Yeast Saccharomyces cerevisiae has a large number of fungal genomes, a relatively small genome (6,000 genes total), and relatively little mRNA splicing.
“To mitigate the first three challenges, we chose to predict protein complexes for yeast Saccharomyces cerevisiae as the starting point because there are a large number of fungal genomes (16), the genome is relatively small (6,000 genes total), and there is relatively little mRNA splicing (17).”
From Computed structures of core eukaryotic protein complexes (2021) · cites this paper as [16]
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“Widespread Occurrence of Fungal Type III PKSs in the Fungal Kingdom Fungal type III PKS protein sequences were retrieved from 1,193 fungal genomes available at the JGI Mycocosm repository (Grigoriev et al., 2014).”
BackgroundMethodSonderegger, C., Váradi, G., Galgóczy, L., Kocsubé, S., Posch, W., Borics, A., Dubrac, S., Tóth, G. K., Wilflingseder, D., & Marx, F. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01655 · Cited by 48 · see citing works
- Authors
- Grigoriev, I. V., Nikitin, R., Haridas, S., Kuo, A., Ohm, R., Otillar, R., Riley, R., Salamov, A., Zhao, X., Korzeniewski, F., Smirnova, T., Nordberg, H., Dubchak, I., & Shabalov, I.
- Affiliations
- Joint Genome Institute (US)
- Corresponding author
- Grigoriev, Igor V.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-12-01
- Volume
- 42
- Issue
- D1
- Pages
- D699-D704
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3965089
- OpenAlex
- W1987916789
- Cited by
- 1,498
- References
- 40
- Citations by year
- 2026: 87 · 2025: 137 · 2024: 151 · 2023: 147 · 2022: 150 · 2021: 187 · 2020: 132 · 2019: 132 · 2018: 122 · 2017: 93 · 2016: 70 · 2015: 66 · 2014: 20 · 2013: 2
- FWCI
- 23.61
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- U.S. Department of Energy (-AC02-05CH11231, 05CH11231, DE AC02 05CH11231, DE-AC02-)
- Office of Science (DEAC02–05CH11231, AC02-05CH11231, DE-AC02)
- Biological and Environmental Research (05CH11231, DE-AC02 − 05CH11231, AC02-05CH11231)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Mycorrhizal Fungi and Plant Interactions
- Keywords
- fungal genomics, fungal genome sequencing, genome annotation, web-based data portal
- MeSH terms
- Fungi, Genome, Fungal, Internet, Genomics, Databases, Genetic, Molecular Sequence Annotation
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